Matsumoto Yukihiro, a.k.a. Matz, visits Biohackathon 2018 !
# | biogem | description | by | cite | version | released | stars | issues | source | build | total | 90d*) | 7d | 90d**) | ||
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downloads | commits | |||||||||||||||
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Bioinformatics library
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BioRuby project |
11 weeks
|
198520
|
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Parser of scientific names
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Dmitry Mozzherin |
|
2 months
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94574
|
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||||||||||
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Binder of samtools for Ruby, on the top
|
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal |
|
11 months
|
67920
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||||||||||
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Blast search made easy!
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Anurag Priyam, Ben J Woodcroft, Vivek Rai et al. |
17 months
|
59204
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Biogem is a software generator for Ruby in
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Raoul J.P. Bonnal, Pjotr Prins |
4 years
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59169
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Shintaro Katayama |
|
22 months
|
45245
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The Ruby ucsc api: accessing the ucsc genome
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Hiroyuki Mishima, Jan Aerts |
7 months
|
41787
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Http requests to entrez e-utilities
|
Jared Ning |
|
3 years
|
37346
|
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||||||||||
|
Create pretty svg-format images of features, gene models
|
Dan MacLean |
|
4 years
|
36033
|
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||||||||||
|
Tool to work with polyploids, ngs and molecular
|
Ricardo H.  Ramirez-Gonzalez |
|
2 weeks
|
|
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32860
|
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A Ruby api for interacting with biomart services
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Darren Oakley |
|
7 years
|
32695
|
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||||||||||
|
Maf parser for BioRuby
|
Clayton Wheeler |
|
6 years
|
30191
|
|
||||||||||
|
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer
![]() |
Pjotr Prins |
3 years
|
28951
|
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|||||||||||
|
Gff3 parser for big data
![]() |
Pjotr Prins |
6 years
|
28111
|
|
|||||||||||
|
A biogem to submit jobs on a queue
|
Francesco Strozzi |
|
6 years
|
26722
|
|
||||||||||
|
Interfaces with biomodel search engine
![]() |
Niall Beard |
|
6 years
|
26391
|
|
||||||||||
|
An open source framework for transforming heterogeneous data
|
Joachim Baran, Kevin B. Cohen, Geraint Duck et al. |
|
3 years
|
24580
|
|
||||||||||
|
Log4r wrapper with extra features for roles and
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Pjotr Prins |
|
6 years
|
23694
|
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||||||||||
|
Ruby parsering for obo files
![]() |
Matt Yoder |
|
7 years
|
23190
|
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||||||||||
|
Data mining algorithms for jRuby
|
arrigonialberto86 |
|
5 years
|
19799
|
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||||||||||
|
Swiss army knife of tabulated data; transforming/filtering tab/csv
|
Pjotr Prins |
|
4 years
|
19633
|
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||||||||||
|
Support for multiple sequence alignments (msa)
|
Pjotr Prins |
|
14 months
|
19532
|
|
||||||||||
|
A fast parser for fastq files
|
Francesco Strozzi |
|
6 years
|
18162
|
|
||||||||||
|
Fast multi-purpose multi-threaded vcf parser
|
Pjotr Prins |
|
2 years
|
16853
|
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|
Ruby parser for fastqc output
|
Tazro Inutano Ohta |
|
4 months
|
16295
|
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|
Rocker
|
Luis (Coto) Orellana, Luis M. Rodriguez-R |
|
5 months
|
|
|
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15632
|
|
0
|
0
|
|||||
|
Basespace Ruby sdk is a Ruby based software
|
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al. |
|
5 years
|
15391
|
|
||||||||||
|
A tool to classify and manipulate pfemp1 dbl-alpha
|
George Githinji |
|
5 years
|
|
|
15245
|
|
||||||||
|
Low memory sequence emitters
|
Pjotr Prins |
|
4 years
|
14838
|
|
||||||||||
|
A wrapper for the signal peptide prediction algorith
|
Ben J Woodcroft |
|
4 years
|
14311
|
|
||||||||||
|
Pipeline to remove contaminations from est libraries
|
Philipp Comans |
|
7 years
|
14237
|
|
||||||||||
|
Bio-ngs provides a framework for handling ngs data
|
Francesco Strozzi, Raoul J.P. Bonnal |
|
6 years
|
14233
|
|
||||||||||
|
Build genome output files
|
Michael Barton |
|
5 years
|
13878
|
|
||||||||||
|
A BioRuby plugin for interaction with the transmembrane
|
Ben J. Woodcroft |
|
20 months
|
13727
|
|
||||||||||
|
A nexus file format (phylogenetic inference) parser in
![]() |
mjy |
|
7 years
|
13627
|
|
||||||||||
|
A biogem for counting small kmers for fingerprinting
|
Ben J Woodcroft |
5 years
|
13487
|
|
|||||||||||
|
Identifying problems with gene predictions
![]() |
Monica Dragan, Ismail Moghul, Anurag Priyam et al. |
3 months
|
13273
|
|
|||||||||||
|
Simple morphbank (http://morphbank.net) services accessor
![]() |
mjy |
|
7 years
|
12490
|
|
||||||||||
|
Ruby wrapper for sambamba tool
|
Artem Tarasov |
|
6 years
|
12415
|
|
||||||||||
|
BioRuby assembly plugin
|
Chase Miller, Francesco Strozzi |
|
7 years
|
12153
|
|
||||||||||
|
Server for polymarker. to be used with cron
|
Ricardo H.  Ramirez-Gonzalez |
|
3 years
|
|
|
12045
|
|
||||||||
|
Parser to work with file formats used in
|
Ben J Woodcroft |
|
3 years
|
|
|
12000
|
|
||||||||
|
Lightweight Ruby api for ncbi eutils
|
Joon Lee, aka seouri |
|
5 years
|
11907
|
|
||||||||||
|
A general purpose framework for scripted handling of
development/stable
|
mjy |
|
5 years
|
11824
|
|
||||||||||
|
A BioRuby plugin for calculating the isoelectric point
|
George Githinji, Pascal Betz |
|
6 years
|
|
|
11684
|
|
||||||||
|
BioRuby plugin for reading and writing nexml (http://nexml.org)
![]() |
Rutger Vos, Anurag Priyam |
|
6 years
|
11541
|
|
||||||||||
|
Reading/writing bgzf blocks
|
Artem Tarasov, Clayton Wheeler |
|
6 years
|
11093
|
|
||||||||||
|
Supports linking of models within a ror application
![]() |
Stuart Owen, Quyen Nguyen |
|
4 years
|
|
|
10600
|
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|
A BioRuby plugin: handling genomic interavals and overlaps
|
Hiroyuki Mishima |
|
7 years
|
10209
|
|
||||||||||
|
Library for visualizing genomic regions
![]() |
Jan Aerts |
|
10 years
|
10130
|
|
||||||||||
|
A web app wrapper for genevalidator
![]() |
Monica Dragan, Ismail Moghul, Anurag Priyam et al. |
3 months
|
9481
|
|
|||||||||||
|
Running and parsing of the protein transmembrane domain
|
Ben J Woodcroft |
|
7 years
|
9311
|
|
||||||||||
|
Read and manipulate cd-hit clusters
|
George Githinji |
|
5 years
|
|
|
9158
|
|
||||||||
|
Retrieve dna sequence from ucsc using given coordinates
|
Andrei Rozanski |
|
3 years
|
|
|
|
8993
|
|
0
|
0
|
|||||
|
A pipeline manager
|
Francesco Strozzi, Raoul Jean Pierre Bonnal |
|
15 months
|
8944
|
|
||||||||||
|
Ruby binding for samtools tabix
|
throwern |
|
5 years
|
8935
|
|
||||||||||
|
Ruby binding for bwa mapping software
|
Francesco Strozzi |
|
7 years
|
8692
|
|
||||||||||
|
Pass a full citation, get the bibtex back,
![]() |
Matt Yoder |
|
9 months
|
|
|
8556
|
|
||||||||
|
A plugin that allows you to parse large
|
robsyme |
|
7 years
|
8372
|
|
||||||||||
|
Bindings to some internals of the velvet assembler
|
Ben Woodcroft |
|
2 years
|
|
|
8218
|
|
||||||||
|
Implementation of the plasmoap algorithm
|
Ben J Woodcroft |
|
2 years
|
8211
|
|
||||||||||
|
Iterate through a samtools pileup file
|
Ben J. Woodcroft |
6 years
|
8197
|
|
|||||||||||
|
Dead simple method of running shell commands from
|
Ben J. Woodcroft |
|
16 months
|
|
|
8099
|
|
||||||||
|
Gene ontology (go) interface for Ruby
|
Ben J Woodcroft |
|
8 years
|
8003
|
|
||||||||||
|
Next-generation mapping of mutations
|
Dan MacLean |
|
6 years
|
7664
|
|
||||||||||
|
Api to ensembl databases
![]() |
Jan Aerts, Francesco Strozzi |
7 years
|
7578
|
|
|||||||||||
|
Timeseries modules for statsample
|
Ankur Goel, Claudio Bustos |
|
5 years
|
|
|
7570
|
|
||||||||
|
Publish scientific results to the semantic web
![]() |
Will Strinz |
|
4 years
|
7528
|
|
||||||||||
|
Ruby wrapper for the gff3-pltools
|
Marjan Povolni |
|
6 years
|
7475
|
|
||||||||||
|
Chembl rest api client, parser and container
|
Mitsuteru Nakao |
|
6 years
|
7353
|
|
||||||||||
|
This biogem is built around krona, a flashy
|
Ben J. Woodcroft |
|
3 years
|
7321
|
|
||||||||||
|
Ruby binding to the ucsc kent utilities
|
throwern |
|
6 years
|
7302
|
|
||||||||||
|
Bioinformatics triple-store support
|
Pjotr Prins |
|
6 years
|
6816
|
|
||||||||||
|
Parse affymetrix cel/cdf files
|
Pjotr Prins |
|
7 years
|
6788
|
|
||||||||||
|
BioRuby plugin for unichem rest web service
|
Mitsuteru Nakao |
|
5 years
|
|
|
6481
|
|
||||||||
|
Geneexpression illuminahumanannotation
|
Raoul J.P. Bonnal |
|
7 years
|
6466
|
|
||||||||||
|
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
|
Andrei Rozanski |
|
4 years
|
6412
|
|
||||||||||
|
Reports whether a nucleotide change results in synonymous
|
Dan MacLean |
|
5 years
|
|
|
6398
|
|
||||||||
|
A protparam compatible utility for BioRuby
|
hryk |
|
5 years
|
5993
|
|
||||||||||
|
BioRuby core plugins, most and stable plugins. blastxmlparser,
![]() |
Raoul J.P. Bonnal |
7 years
|
5833
|
|
|||||||||||
|
Enables the localisation predictor wolf psort to be
|
Ben J Woodcroft |
|
6 years
|
5630
|
|
||||||||||
|
Programmatic interface to the cnls nuclear localisation signal
|
Ben J. Woodcroft |
|
6 years
|
5604
|
|
||||||||||
|
Fast download blast databases from ncbi
beta
|
Anurag Priyam |
|
19 months
|
5323
|
|
||||||||||
|
Parse pfam hmm definition files
|
Ben J. Woodcroft |
6 years
|
5182
|
|
|||||||||||
|
Bio-gag is a biogem for detecting and correcting
|
Ben J Woodcroft |
6 years
|
5069
|
|
|||||||||||
|
Biostars data-mining and statistical analysis
|
Joachim Baran |
|
4 years
|
|
|
4888
|
|
||||||||
|
Fast storage and comparison of chr+pos(+alt) locations
|
Pjotr Prins |
|
3 years
|
4687
|
|
||||||||||
|
Client for xoopit's cloudquery api
|
Cameron Walters, nb.io |
|
9 years
|
4660
|
|
||||||||||
|
A sequence read archive (sra) download script and
|
Ben J. Woodcroft |
|
2 years
|
4609
|
|
||||||||||
|
Enables parsing of hmmer version 3 reports
|
Christian Zmasek, Ben J Woodcroft |
3 years
|
4315
|
|
|||||||||||
|
Gggenome Ruby client
|
Mitsuteru Nakao |
|
5 years
|
4113
|
|
||||||||||
|
Ruby ensembl rest api
|
Alberto Donizetti |
|
5 years
|
4069
|
|
||||||||||
|
Csshttprequest is cross-domain ajax using css as a
|
Cameron Walters, Randy Reddig |
|
9 years
|
3957
|
|
||||||||||
|
Generalized linear models for statsample
|
Ankur Goel |
|
5 years
|
|
|
3952
|
|
||||||||
|
Rubybhl is a simple request/response wrapper for the
![]() |
Matt Yoder |
|
4 years
|
3899
|
|
||||||||||
|
Helper methods for reading .delta files
|
robsyme |
|
3 years
|
|
|
3772
|
|
||||||||
|
Interface for express beta diversity
|
Ben J. Woodcroft |
|
4 years
|
|
|
3732
|
|
||||||||
|
Bio-repeatmasker
|
Andrei Rozanski |
|
4 years
|
3664
|
|
||||||||||
|
A programmatic interface to the ipcress in-silico pcr
|
Ben J Woodcroft |
|
23 months
|
3591
|
|
||||||||||
|
A parser for cigar format alignments
|
Ben J Woodcroft |
|
4 years
|
3546
|
|
||||||||||
|
BioRuby plugin for sun grid engine
|
Toshiaki Katayama |
|
7 years
|
3493
|
|
||||||||||
|
Web server for bio-samtools
|
homonecloco |
|
4 years
|
|
|
3443
|
|
||||||||
|
Hello world plugin for the BioRuby (just for
|
Toshiaki Katayama |
|
7 years
|
3438
|
|
||||||||||
|
Digests dna based on restriction enzyme cut patterns
![]() |
Trevor Wennblom |
7 years
|
|
|
3385
|
|
|||||||||
|
Emulates as if old BioRuby biofetch alives
|
Naohisa Goto |
|
2 years
|
|
|
3337
|
|
||||||||
|
Does high pairwise alignment of sequencing reads with
|
John T. Prince |
|
8 years
|
3317
|
|
||||||||||
|
A method to get the nucleotide sequence of
|
Ben J Woodcroft |
|
7 years
|
3211
|
|
||||||||||
|
BioRuby core ext: plugins which require external library
![]() |
Raoul J.P. Bonnal, Pjotr Prins |
7 years
|
3175
|
|
|||||||||||
|
Meta package for biolinux distribution
![]() |
Raoul J.P. Bonnal |
|
7 years
|
3170
|
|
||||||||||
|
Restriction enzyme dataset
![]() |
Sir Richard J. Roberts, Trevor Wennblom |
7 years
|
|
|
3128
|
|
|||||||||
|
A Ruby api to the ensembl database
![]() |
Jan Aerts, Francesco Strozzi |
7 years
|
3128
|
|
|||||||||||
|
One-line summary of your gem
|
Toshiaki Katayama |
|
7 years
|
3122
|
|
||||||||||
|
Decoding the dbsnp bitfield
|
Hiroyuki Mishima |
|
7 years
|
3099
|
|
||||||||||
|
Hydropathy scale for BioRuby
|
Ben J Woodcroft |
|
6 years
|
3066
|
|
||||||||||
|
Phyloxml plugin for BioRuby
|
Diana Jaunzeikare, Clayton Wheeler |
|
6 years
|
3046
|
|
||||||||||
|
Wrapper around the exportpred algorithm for predicting p
|
Ben J Woodcroft |
|
6 years
|
3042
|
|
||||||||||
|
Biological extensions for the intermine webservice client library
|
Alex Kalderimis |
|
7 years
|
3037
|
|
||||||||||
|
A simple biogem that allows computation of the
|
Ben J Woodcroft |
|
6 years
|
3035
|
|
||||||||||
|
Build graph with jRuby
|
Matteo Picciolini |
|
6 years
|
|
|
2965
|
|
||||||||
|
Reads metadata from integrated microbial genomes (img) metadata
|
Ben J. Woodcroft |
5 years
|
|
|
2628
|
|
|||||||||
|
Aggregate fastqc (quality control for next generation sequencing
|
Raoul Jean Pierre Bonnal |
|
3 years
|
|
|
2592
|
|
||||||||
|
The api for freebayes version #{bio::freebayes::extversion}
|
Natapol Pornputtapong |
|
3 years
|
|
|
|
2529
|
|
0
|
0
|
|||||
|
Parse stockholm sequence alignment format
|
Ben J. Woodcroft |
|
5 years
|
2473
|
|
||||||||||
|
Ruby wrapper to run standard-raxml for maximum likelihood
|
Fernando Izquierdo |
|
5 years
|
|
|
2361
|
|
||||||||
|
Ruby inferface for kseq.h by heng li for
|
Fedor Gusev |
|
4 years
|
2167
|
|
||||||||||
|
Mine publications for gene names
|
Pjotr Prins |
|
4 years
|
1971
|
|
||||||||||
|
A Ruby wrapper on the open tree api
beta
|
Matt Yoder |
|
4 years
|
1883
|
|
||||||||||
|
A restful service for sharing genomic data
![]() |
Joachim Baran, Robert Buels, Michel Dumontier |
|
4 years
|
|
|
1812
|
|
||||||||
|
Tools to work with fasta files, indexed with
|
homonecloco |
|
4 years
|
|
|
1805
|
|
||||||||
|
gemma with loco and permutations
|
Pjotr Prins |
|
3 weeks
|
|
|
1779
|
|
||||||||
|
Tools to manipulate blat files from the command
|
homonecloco |
|
4 years
|
|
|
1772
|
|
||||||||
|
Faldo location output method for bio::location in BioRuby
|
Joachim Baran, Naohisa Goto |
|
4 years
|
|
|
1737
|
|
||||||||
|
Api of picard tool
|
Natapol Pornputtapong |
|
3 years
|
|
|
|
1653
|
|
0
|
0
|
|||||
|
A Ruby wrapper for bio sparql service
|
Natapol Pornputtapong |
|
3 years
|
|
|
|
1597
|
|
0
|
0
|
|||||
|
Csshttprequest is cross-domain ajax using css
disabled
|
Cameron Walters, Randy Reddig |
|
9 years
|
|
|
|
1549
|
|
0
|
0
|
|||||
|
Tools for jaspar motifs in BioRuby
|
Jessica Lee, Wasserman Lab |
|
3 years
|
|
|
1377
|
|
||||||||
|
Basic wrapper for the kallistio mapper
|
homonecloco |
|
3 years
|
1371
|
|
||||||||||
|
A pipeline creator for BioRuby
|
Natapol Pornputtapong |
|
3 years
|
|
|
|
1367
|
|
0
|
0
|
|||||
|
Methods for handling multiwell plate annotations
|
Steve Pettitt |
|
2 years
|
|
|
1191
|
|
||||||||
|
Parsing and mutation calling from sam, cigar and
|
Stephen Pettitt |
|
2 years
|
|
|
1131
|
|
||||||||
|
Biosql plugin for BioRuby
|
BioRuby project |
|
2 years
|
|
|
915
|
|
||||||||
|
BioRuby shell: interactive analysis environment for BioRuby
|
BioRuby project |
|
15 months
|
|
|
511
|
|
||||||||
|
BioRuby executables: utilities bundled with BioRuby
|
BioRuby project |
|
15 months
|
|
|
504
|
|
||||||||
|
pre
|
|
|
|
|
0
|
|
*) gem downloads (total & last 90 days) from
rubygems.org
as of
2018-12-11
**) number of commits on GitHub (last 7 days & last 90 days)
**) number of commits on GitHub (last 7 days & last 90 days)